The version that is run is the one that is represented by the yourapp.application file in the top level of the directory structure for the deployment. I am assuming that you are retaining the directory structure as if you were publishing directly to the server, and you have folders for each version deployed.
If you are doing that, then you can copy the yourapp.application file from the folder for that version and put it in the top level, called yourapp.application (i.e. remove the version in the name if it's in there (vs2005)), replacing the one that is there.
If you are using a publish.htm file, you'll need to edit that to change the version.
If someone has version 1.0.10, and you change the current version to 1.0.9, and it is online-only, I think it will install 1.0.9 again. You'll have to try that out.
If it is online/offline, and you are not pushing the updates as required, they will have to uninstall and select to go back one version.
RobinS.
GoldMail.com